From ab4a9fa64fd2676ceea0f1d738590a4cc66e825f Mon Sep 17 00:00:00 2001 From: Ron Levine Date: Fri, 6 Jan 2017 17:15:56 -0500 Subject: [PATCH] Update stand_call_conf doc strings --- .../GenotypeCalculationArgumentCollection.java | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/arguments/GenotypeCalculationArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/arguments/GenotypeCalculationArgumentCollection.java index ed639c951..e683ec130 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/arguments/GenotypeCalculationArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/arguments/GenotypeCalculationArgumentCollection.java @@ -101,9 +101,13 @@ public class GenotypeCalculationArgumentCollection implements Cloneable{ public double heterozygosityStandardDeviation = 0.01; /** - * The minimum phred-scaled Qscore threshold to separate high confidence from low confidence calls. Only genotypes with - * confidence >= this threshold are emitted as called sites. A reasonable threshold is 30 for high-pass calling (this - * is the default). + * The minimum phred-scaled confidence threshold at which variants should be called. Only variant sites with QUAL equal + * or greater than this threshold will be called. Note that since version 3.7, we no longer differentiate high confidence + * from low confidence calls at the calling step. The default call confidence threshold is set low intentionally to achieve + * high sensitivity, which will allow false positive calls as a side effect. Be sure to perform some kind of filtering after + * calling to reduce the amount of false positives in your final callset. Note that when HaplotypeCaller is used in GVCF mode + * (using either -ERC GVCF or -ERC BP_RESOLUTION) the call threshold is automatically set to zero. Call confidence thresholding + * will then be performed in the subsequent GenotypeGVCFs command. */ @Argument(fullName = "standard_min_confidence_threshold_for_calling", shortName = "stand_call_conf", doc = "The minimum phred-scaled confidence threshold at which variants should be called", required = false) public double STANDARD_CONFIDENCE_FOR_CALLING = 10.0;